Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
Space Filling Model

Packages

 Space_filling_model_coarse_graining
 Space_filling_model_coarse_graining is a package of applications proposing various volume based geometric approximation schemes to coarse grain molecular models defined by unions of balls.
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Space_filling_model_interface
 Space_filling_model_interface is a package of applications to model interfaces within a macro-molecular assembly, at atomic or coarse grain resolution. The interface particles are reported, together with a number of geometric, topological and bio-physical statistics describing the interfaces.
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Space_filling_model_interface_finder
 Space_filling_model_interface is a package proposing algorithms to automatically identify all the interfaces present in a molecular structure. Interfaces may be sought between different chains or between regions of different chains. The interface identified by Space_filling_model_interface_finder may be further analyzed with applications of the package Space_filling_model_interface.
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Space_filling_model_shelling_diagram_comparison
 Space_filling_model_shelling_diagram_comparison is a package of applications focusing on the comparison of binding patches as computed in Space_filling_model_shelling_diagram_surface_encoding. In particular, the binding patches may be compared from a geometric of topological standpoint, the latter being more lenient than the former.
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus and N. Malod-Dognin

 
 Space_filling_model_shelling_diagram_surface_encoding
 Consider a binding patch i.e.. the atoms of a complex directly in contact with a partner. Space_filling_model_shelling_diagram_surface_encoding is a package providing several encodings of a binding patch, and notably the atom shelling tree, which generalizes core-rim models. Binding patches can be compared using the applications of Space_filling_model_shelling_diagram_comparison.
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus

 
 Space_filling_model_surface_volume
 Space_filling_model_surface_volume is a package of applications providing numerically certified estimates of the surface area and of the volume of a model defined by a collection of balls, e.g. a van der Waals or solvent accessible model.
Reference ManualUser Manual . Authors: F. Cazals and T. Dreyfus and S. Loriot

 

Description

Applications dealing with molecular geometric models defined by union of balls.